How to get all of the subjects of a Jena Query?

Interesting question. What you need to do is go through the query, and for each block of triples iterate through and look at the first part.

The most robust way to do this is via an element walker which will go through each part of the query. It might seem over the top in your case, but queries can contain all sorts of things, including FILTERs, OPTIONALs, and nested SELECTs. Using the walker means that you can ignore that stuff and focus on only what you want:

Query q = QueryFactory.create(query); // SPARQL 1.1

// Remember distinct subjects in this
final Set<Node> subjects = new HashSet<Node>();

// This will walk through all parts of the query
ElementWalker.walk(q.getQueryPattern(),
    // For each element...
    new ElementVisitorBase() {
        // ...when it's a block of triples...
        public void visit(ElementPathBlock el) {
            // ...go through all the triples...
            Iterator<TriplePath> triples = el.patternElts();
            while (triples.hasNext()) {
                // ...and grab the subject
                subjects.add(triples.next().getSubject());
            }
        }
    }
);